It seems that during the breakup of Yugoslavia there were civil wars during speakers of the (then officially) same language - Serbs, Croats and Bosniaks, but not, e.g., between Serbs and Slovenians. Is there any specific reason for this?

Just a small point of correction. There has been fighting in post-Yugoslavia Macedonia. The country has a sizable Albanian minority and some fairly serious (albeit short-lived) clashes have occurred between them and the government.
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SigueSigueBenDec 7 '11 at 20:49

5 Answers
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Among other (geostrategic) reasons, the most plausible explanation is because in Bosnia & Herzegovina and Croatia there were regions in which considerable Serb populations had lived since long ago (for example in Krajina in Croatia from the 16th century). During a hegemonic treatment of other nations in the second Yugoslavia, the Serbs slowly planned and succeeded in populating these base Serb regions with more of their countrymen from Serbia. In the late 80s, these Serb populations were an argument to seize the land and form Great Serbia.

During the war, these factions were funded and supplied from Belgrade. It was much easier to maintain strategic control from regions where the people directly supported the army (which was completely Serb at the time of Yugoslav breakup). That is why the Serbs concentrated their efforts on Croatia and Bosnia, withdrawing all tanks and military from Slovenia, for example. If they had won the war, I assume that the international community would have completely accepted their idea to reoccupy Slovenia and Macedonia as well, under the name of Yugoslavia. Also, I assume that a condition for doing that would have been that they cling to the EU/US, and not Russia.

I think the perception of each other was the key issue there. Serbs view Slovenians and Macedonians as separate people (something like Russians view Estonians), so there wasn't that much of emotion when Slovenians declared independence (there was a brief intervention though).

However Croatian independence was a completely different story. Serbs had the idea of slav unity, and Croats were the integral part of this idea. Serbs did not accept the Croatian independence mainly because of that. A long trail of controversial historic events between two nations, religion contributed to the animosity between the two nations.

To understand my answer you need to get back to 1844., when Ilija Garašanin wrote Načertanije. In that document he made base plan of making Greater Serbia. Greater Serbia should include Serbia, Bosnia and Herzegovina, big part of Croatia, Montenegro and Northern part of Albania. That idea was revived by Stevan Moljević, Serbian Chetnik who wanted to clean up parts of holy Serbian land (term which was used by Chetniks, reffers to Greater Serbia) from Croatians, Bosniaks and other people who weren't Serbs. In late 1980's head of Serbian communists became Slobodan Milošević who had views similar to Stevan Moljević and Ilija Garašanin. He wanted to finnaly achieve making of that country. However, Slovenia and Macedonia were not imagined as parts of Greater Serbia, as Croatia and Bosnia Herzegovina was. So there was great war between Serbs and Croats and Bosniaks and Serbs. There was war between Slovenian people and Serbs, but as Slovenia wasn't so important for making Great Serbia, war ended very fast.

As stated by others this is not really true. Even though shorter and less bloody compared to those in Bosnia and Croatia, the 10-day war outbroke in Slovenia between Yugoslav army located in the province and Slovenian police forces.

To answer your question: the reason perhaps lies in the fact that Slovenia had ethnically clear picture with majority of Slovenians living within its border, i.e. the Slovenian border encompass Slovenian people quite fairly. On the other hand, Croatia had around 20-25% Serbian population when the war escalated in 1991. Bosnia had even worse mixture of three ethnic groups: Muslims 40% (nowadays called Bosniaks to distingish them from Bosnians which might refer to all people in Bosnia and Herzegovina), Serbs 40% and Croats 20%. These numbers are out of my head and might not be as accurate but rough approximations. Of course mixed marriages and people declaring as Yugoslavians were present all around the ex-Yugoslavia and especially in Bosnia.